Goodbyes Don't Last Forever
by Anoveldebut
Summary: What if the team had gone back for Elizabeth at the end of "Ghost in the Machine"? Could they have saved her? This is my AU take on the end of that episode, and everything that followed. [Pairings: Mckay/Keller, John/Elizabeth]
1. Chapter 1

**Setting: This story picks up at the end of "Ghost in the Machine" (Season 5) and carries through to the end of the series. It's an AU, because, let's face it, Elizabeth deserved a better ending. So here's my take on things.**

 **Disclaimer: I own nothing, and make absolutely no money from doing this.**

 **Reviews: Feebback is always welcome! This is my first SGA fic, so I look forward to hearing what you think!**

* * *

 **Chapter One**

 **[Post "Ghost in the Machine"]**

Rodney returned to his lab, miserably alone and empty.

Either way, they would have lost her. Logically, he knew that. But it still felt like his fault.

He sank into his chair, staring dejectedly at his computer screen.

Reactivating the nanites had seemed like such a good idea at the time. Brilliant, in fact, given that it wasn't entirely his own. Sheppard had told him it was a bad idea. Elizabeth had agreed, after the fact. But he'd never believed until the moment they'd lost her on the Replicator planet.

And now, now...

They'd just lost her again.

Rodney sank against his desk, head in his hands. He'd never felt guiltier about anything in his life.

His computer beeped. Rodney ignored it. What was the point, anyway?

"I don't have much time, Rodney, but there's still a chance."

The voice was urgent, pressing even, but more importantly, it was _hers_.

"Elizabeth?," he asked, looking up.

"You and your team can still complete what we've begun. Not for all the Replicators, but...," she paused, the image of Fran on his screen looking oddly uncertain for someone usually so confident. "For me," she finished, her face a mixture of embarrassment and pleading. "Please, Rodney. You have the skills. You can download my consciousness into an isolated storage device, keeping the rest of Atlantis safe. Then, when you're ready, you can transfer it into the new human form."

Rodney's mind was reeling. _Create a machine that would make a human body?_ It was ambitious, even for him.

"My fate is in your hands," she said, the image going black.

 _Oh crap._

* * *

"Dr. McKay?," Woolsey asked, looking up from his desk.

"You're not going to like this, but I need to show you something," Rodney said, setting down his laptop. He hit play, and Elizabeth's message began.

Mr. Woolsey pursed his lips, watching it silently to the end.

"Is this possible?," he asked, looking to McKay.

"I don't know," Rodney replied, nervous. "Maybe. It's Ancient technology. We have the schematics. But it's not going to be easy."

"Have you talked to Sheppard yet about the logistics of even retrieving her consciousness?," he asked.

"Are you kidding?," Rodney demanded. "Sheppard and Elizabeth...they were close. No way am I bringing this to his attention without knowing we can pull it off."

Woolsey considered. "I don't object to the idea of saving one of our own people," he said softly. Rodney nodded. "Make the preparations for a virtual reality," Woolsey decided. "Once we have a safe place to put her, then we can bring the rest of your team in to confer."

"Okay," Rodney nodded, retreating.

"And Dr. McKay?"

"Yes?," he asked nervously.

"Have some sort of interface ready so we can be sure it really is Elizabeth Weir before we give her a new body."

"Right. Okay," he said, suddenly on a mission.

* * *

"John, you should not be alone with your thoughts," Teyla said softly, stepping up beside him at the balcony rail.

John closed his eyes, focusing on the sounds and smells of the ocean all around.

"Dr. Weir was a friend to us all," Teyla remarked. "You are not alone in missing her."

John didn't answer. Teyla sighed.

"She is not dead, John. From what we know of the Replicators, they can survive even the harsh conditions of space for a time. There may still be hope."

John turned to her, chest tight. "Woolsey would never agree."

"Not without a plan," Teyla conceded. "So make a plan, John. Come up with a means to save her, without alerting the other Replicators."

"We still don't even know for sure if that _was_ Elizabeth," he said bitterly, the hope in his eyes fading.

"She sacrificed herself to save Atlantis," Teyla replied evenly. "I believe it _was_ Dr. Weir."

"She was also the one who led the Replicators here in the first place," John pointed out angrily. "She _lied_ to us, Teyla."

"So you do not believe that was the real Elizabeth?," she asked cautiously.

"I don't know," he answered tightly, turning back to the water.

"You knew her better than any of us," Teyla conceded softly. "Although I do not believe it is entirely out of character for Dr. Weir to want to help the Replicators achieve Ascension. It is a worthy goal, and a peaceful alternative to Oberoth's policies."

"Teyla?," John called, just as she was turning to leave.

"Yes?"

"What do Ronon and Mckay think?"

"None of us were convinced until she stepped through the gate. But her sacrifice...it speaks for itself."


	2. Chapter 2

**A/N: Thank you _so_ much to everyone who has reviewed so far! Your enthusiasm for this story has really made my week!**

 **Here's the next chapter, and I hope you all enjoy!**

* * *

 **Chapter Two**

Mr. Woolsey had assembled everyone he'd requested, Rodney noted with satisfaction, pacing around the room. Sheppard, Teyla and Ronon, of course, but also Colonel Cauldwell, Zalenka, and Dr. Keller. As Mr. Woolsey took his seat, Rodney began.

"After our last encounter with the Replicators, I returned to my lab to find _this_ ," he said, hitting play so that everyone could watch Elizabeth's message on a central screen.

"Why am I just seeing this _now_?," Sheppard demanded, rounding on the scientist.

"Because we needed a plan," he answered evenly, hitting a few more keys on his computer. The model for his virtual reality Atlantis came up on the screen.

"I take it that's your virtual reality?," Mr. Woolsey asked.

"Yes," Rodney confirmed. "I have it on a small system completely isolated from the others, powered by it's own Naquadah generator. It has more than enough capacity to house Elizabeth's full consciousness, while simultaneously supporting external visits from, say, any one of us. I've also taken the liberty of connecting an EEG machine to the system in order to monitor the brainwave activity of anyone who goes in there, as well as Elizabeth herself. We're hoping that with this addition, and our own knowledge of Elizabeth's personality, we'll be able to determine once and for all if the Replicator was telling the truth, and if so, finish the work she began."

"I have copies of all of Dr. Beckett's scans from the original Dr. Weir," Dr. Keller confirmed, catching on. "It shouldn't be too hard to compare what we have on file to what we find in this system."

"I was hoping you'd say that," Rodney said, beaming.

"How do you intend to rescue this Replicator without having to contend with any of the others?," Cauldwell asked, crossing his arms to glare suspiciously at McKay.

"That's where you come in," Rodney announced. "Using the Asgard beaming technology onboard the Odyssey, we're going to beam the frozen Replicator onboard, download her entire consciousness onto the virtual system, and then beam her back into space, without ever reactivating her."

"You can do that?," Cauldwell asked doubtfully.

"Theoretically, yes," Rodney replied.

Zalenka pushed his glasses up the bridge of his nose. "Even a computer needs to be turned on before it's data can be accessed," he pointed out. "Downloading a human consciousness from a machine will be far more difficult."

"Look, her body may be frozen in space, but her brain should still be active. All I'll need to do is set up my interface and download her consciousness directly from the Replicator's head into the virtual reality."

"And if things don't go according to plan?," Sheppard asked bitingly. "Then what? We abandon her? Or we risk reactivating her to get what we want?"

"We could set up a containment field while Rodney works," Zalenka mused. "That way the Replicator will pose no threat to the rest of the ship."

"Just Rodney?," Sheppard asked, considering.

"Yes," Zalenka confirmed.

Rodney glared at the pair of them.

"Just how do you propose we get a transport lock on her?," Cauldwell asked. "Our scans won't be able to differentiate between one Replicator and the next."

"Yes they will," Rodney replied triumphantly. "When Elizabeth took Replicator form, she used my FRAN template. I can recalibrate the Odyssey's sensors to scan for an exact match, and we can go from there."

"Dr. Zalenka, how much time will you need to set up the containment field?," Woolsey asked.

"A few hours. Six at most," the scientist assured.

"We'll have it done in four," McKay countered.

"So we're really doing this?," Ronon asked.

"Unless someone has a reason why we shouldn't?," Woolsey replied, looking around. No one spoke. "Then we're really doing this," he confirmed.

* * *

John cornered the scientist in his lab, all but pinning him to the wall.

"What was the real reason you held out on me?," he demanded, staring Rodney square in the eye.

Rodney squirmed uncomfortably. "This," he squawked, glancing meaningfully at John's imposing posture.

" _Rodney_ ," John warned.

"You were closer to Elizabeth than anyone else here," the scientist babbled. "I just...I didn't want to get your hopes up until I was sure we could actually do this."

"And can we, Rodney? Can we actually pull this off?," the Colonel demanded.

"At least as far as getting her into the virtual reality goes and verifying that she _is_ Elizabeth Weir, yes," the scientist confirmed, not a trace of doubt in his voice. "The rest might be a little complicated."

"Rodney."

"Look. Woolsey gave me the go-ahead two weeks ago. I've worked out the details for phase one of our plan, but phase two is still a little fuzzy. I'll get on it once we have Elizabeth safely back on Atlantis."

"And if it isn't Elizabeth?"

"Then we scrap the system and go back to missing her every single day," Rodney said softly. "But John, I'm pretty sure it _is_ Elizabeth."

"Was there anything else to that message?," John asked, backing off a little as the scientist readjusted himself to a more comfortable position.

"No. Just what I showed everyone in the briefing."

"All right, then," John said, a flash of disappointment washing over his face before he managed to school his features once more. "Then I guess you'd better get to work."


	3. Chapter 3

**A/N: A short update today, but chapter four will be considerably longer. Thank you again for the reviews!**

* * *

 **Chapter Three**

"All right, we're set with the scanners. Radek..."

"One moment," the scientist replied, rapidly coding something into the computer system. "There. Containment field is ready."

Rodney hit his ear comm. "We're all set down here," he advised.

"Understood," crackled Cauldwell's reply.

A flash of light engulfed Rodney as the FRAN Replicator was beamed into the containment field alongside him.

"We've got her," Rodney called triumphantly, wasting no time in placing the electrodes around the AI's head, setting up the data transfer process.

Outside the containment field, Sheppard and his team of marines raised their weapons to the ready. Rodney tried to ignore them. Tapping a few commands into his computer, the transfer began.

"How long?," Sheppard asked, gaze never wavering from the AI.

"Fifteen minutes," Rodney replied, carefully monitoring the preliminary readings from the transfer. "Jennifer, what are you seeing on the EEG so far?"

"Nothing recognizable, yet," she replied, checking the data streaming across her own screen.

The minutes ticked by. Jennifer nodded. "These are definitely brain wave patterns," she said, to Rodney's relief.

"Good, good," he muttered, checking his own readings. The transfer was nearly complete. "Just a couple more minutes..."

As the last remaining seconds ticked down, Rodney reached toward the inert Replicator, gently removing the electrodes. "Jennifer?"

"It's her!," the doctor crowed, grinning at him through the containment field. "I can confirm a match with Dr. Weir."

"Bridge, this is Sheppard. Ready to beam the Replicator back into..."

"Gawk!," Rodney chocked, cutting off the Colonel's order. Eyes open in a fiery glare, the AI had a hand around his throat, slowly squeezing the life out of him.

"Belay that, bridge!," Sheppard yelled, motioning for Radek to lower the containment field and the marines to move in. Rodney clamped his eyes shut as the firing began, concentrating on staying alive in the Replicator's unforgiving grasp.

The shots couldn't kill the Replicator, of course, but they did seem to distract her. Struggling free, Rodney pulled away, gasping.

"NOW!," Sheppard shouted into his comm, and the Replicator was beamed back into space. "What the hell was _that_?," he demanded, rounding on Rodney.

"It must have been an autonomic response to our perceived attack," Zalenka replied. "A base function of the nanites themselves."

" 'Xactly," Rodney gasped, pointing at Radek.

"Come on, we need to get you to the infirmary," Jennifer replied, taking some of Rodney's weight against her shoulder as he struggled for air.

"Zalenka," Sheppard began.

"Yes, yes. I will double check our systems and make sure the virtual reality holds," he replied, busying himself with the task.

"The slightest hiccough and I want that thing beamed out into space," Sheppard ordered, turning to leave.

"John," Teyla protested, moving toward him.

"I don't want to hear it," he growled, marching from the room.

* * *

"I think you'll live," Keller said, having checked him over for signs of a crushed windpipe. "Though it'll probably hurt to talk for a few days."

"Sheppard doesn't believe us," Rodney croaked, stunned.

"Well, it's a lot to take in, all at once," Dr. Keller replied softly, meeting his gaze. "And he and Dr. Weir were very close. It's hard enough to say goodbye to someone you care about, let alone believe they might come back to you after all this time."

"But you believe?," he asked.

"Yes, Rodney. I believe," she answered, smiling. "Just give the Colonel some time. He'll come around."


	4. Chapter 4

**A/N: Thank you again to everyone reading, reviewing, and enjoying! It means a lot!**

* * *

 **Chapter Four**

 **[Assumes general series knowledge...spoilers for various episodes throughout]**

Elizabeth found herself alone in a corridor on Atlantis. Taking a moment to get her bearings, she headed for the control room, hoping to find some answers.

 _Had Rodney received her message?_ , she wondered. It seemed almost too good to be true, but she couldn't see a reason for the other Replicators to recreate Atlantis just to trick her. If they were capable of revenge, she imagined it would be much more tortuous than this.

Elizabeth scanned the deserted hallways, looking for any sign of life. There didn't seem to be a single soul around.

 _Some welcome home_ , she mused sadly, climbing the last of the stairs to the control tower, and her office. _Woolsey's office,_ she corrected _._

Oddly enough, that last thought bothered her a lot less than it might have when the Replicators had first taken her, nearly two years ago. So much had happened since then. So much had changed.

She meandered back through the halls, checking the gym, the commissary, and the crew quarters.

All were empty.

"Rodney," she whispered. "Where have you brought me?"

* * *

"So who's gonna go in first?," Ronon asked, looking around the room.

"I will," Rodney said, beating Woolsey to the punch. He could just imagine the questions their new expedition leader might have for Elizabeth, and he figured he owed it to her to let her see a familiar face first.

Sheppard, for his part, had refused to come at all. Which left Rodney, Teyla and Ronon as the closest friends she had on Atlantis.

Keller stepped up to him, placing the electrodes around his head. "Whenever you're ready," she said, indicating the gurney they'd set up for visitors to lay on while in the virtual reality.

"Right," Rodney said, laying down. Closing his eyes, he could feel Keller activating the link, and then he was there, in the virtual Atlantis.

"Rodney!," Elizabeth exclaimed, startled.

"Uh, hi," he replied, nervous.

Elizabeth closed the distance between them, wrapping him in her arms. "You have no idea how good it is to see a friendly face," she explained, pulling away.

"I thought...I thought programming expedition members into the virtual reality would be an insult to your intelligence," he babbled. "So I left you with books, movies and music to keep you company."

"I noticed," she said, smiling. "A dog may have been nice as well."

"Oh."

"So this is a virtual reality?," she asked, pushing past the awkward.

"Yes. We needed a safe place to house your consciousness until a body could be made," he answered, still nervous.

"I understand."

"Look, Elizabeth. I never had the chance to say this, but I'm really, really sorry about everything that's happened..."

"I know you are, Rodney," she interrupted, placing a soothing hand on his arm. "And I don't blame you. You were only trying to help."

"It's my fault you were captured by the Replicators."

"And now you're helping me find a way to reclaim my life."

"I really...I really never meant for things to go the way they did."

"I know, Rodney. It's all right."

"It could take a very long time to finish what you asked of me in your message."

"I know."

"Were you serious about wanting a dog? I could program one in..."

"Rodney, sit down with me. Visit."

"I'm not very good at visiting."

"I've noticed," she said, smiling. "How is everyone else doing with all of this?"

"Cautiously optimistic might be the best description," Rodney confessed. "Dr. Keller managed to confirm that you are who you say you are, but it's a lot to take in. Sheppard...Sheppard isn't handling it well."

She nodded. "I wouldn't expect John to trust me yet, not after the role I played with the Replicators."

"Why did you do it?," Rodney asked, before he could stop himself.

"I truly believed they wouldn't pose a threat to Atlantis," Elizabeth answered, smiling wanly. "Their goal was Ascension. They needed your help. I never thought...I never thought they'd put the city in danger the way they did. And I can understand how John would mistake my motives for some sort of Replicator trick, given everything that happened. They weren't supposed to show up until after I'd managed to explain myself."

"Jennifer thinks he'll come around."

"Jennifer?"

"Dr. Keller," he clarified.

"I wasn't aware the two of you were on a first name basis," Elizabeth smiled.

"I...we...," Rodney stuttered.

"Are you an item?," Elizabeth pressed, good humour dancing in her eyes.

"No," he answered quickly. "Just...I don't know. Friends, maybe?"

"Friends, maybe?," Elizabeth parroted. "Rodney, if you like her, you should let her know."

"It's really not that simple."

"It really is," Elizabeth laughed.

"Look, maybe for men like Sheppard or Ronon, but guys like me...it's never that easy."

"Rodney. The only thing John and Ronon have when it comes to women that you _don't_ is confidence."

"And good looks," Rodney corrected forlornly. "Even my own _sister_ told me not to be too picky, because, in her words, I'm 'no John Sheppard.'"

Elizabeth bit back a smile. "Jeannie really said that?"

"Unfortunately, yes," Rodney confessed.

Elizabeth sighed fondly. "I think Dr. Keller would be lucky to have you."

"Yeah, phobias, pessimism, arrogance and workaholism all rolled into one. Who wouldn't want _that_?"

"You're a decent man, Rodney. Shortcomings and all."

"Well...thank you," he replied awkwardly.

"Are you working on anything interesting these days?," she asked.

"You mean aside from this? Nothing much," he answered with a shrug. "Something breaks, I fix it. The world needs saving, I save it. Same old."

"It's nice to see that nothing's really changed since I've been gone," she answered wryly.

"I wouldn't say 'nothing'," he countered. "I mean, Teyla's a whole new force to be reckoned with now that she's a mom. And Woolsey...Woolsey's not as bad from this side as he always seemed from Earth. Actually, even Sheppard has reformed somewhat. I haven't had cause to make fun of his chronic Kirk-isms in ages," Rodney babbled.

Elizabeth smiled.

"You missed Sam too. She was leader of Atlantis for about a year, before Woolsey came."

"Sam Carter?," Elizabeth guessed.

"Mmm. It's actually her fault I had the time to get to know Dr. Keller a bit better."

"Oh?"

"Yeah. See, we were on this planet, an old mining settlement, and I fell down a hole."

Elizabeth frowned.

"Sam and Jennifer were with me. Sam tried to help me out, but the ground collapsed beneath her, bringing both of them down into the mine as well."

"How long were you down there?," Elizabeth asked.

"Long enough," Rodney replied, mentally recoiling from their close call. "But we talked, while we were down there. And took turns saving each other's lives."

"It sounds like quite the experience."

"It was," Rodney replied. "And it was the first time I stopped seeing Sam as the woman of my dreams, and started to think maybe..."

"Maybe someone else would suit you better?," Elizabeth guessed when he didn't finish.

"Yeah."

"That's kind of how I felt the last time we were back on Earth," Elizabeth said candidly. "Simon had already moved on, but it was the first time I really took the time to evaluate my life without him."

"Oddly complete, even without the dream?," Rodney guessed.

"Exactly," Elizabeth replied, smiling.


	5. Chapter 5

**A/N: In response to one of ch 4's guest reviews, no, I am not the same writer as Follow-ur-Shadow. I've read a couple of his/her stories though, and they were _fantastic_. The comparison is flattering, but we're definitely two separate entities. :-) (And for anyone else looking for excellent Sheppard/Weir stories, check out Follow-ur-Shadow's profile. You won't be disappointed :-) )**

 **Thank you as always to everyone reading and reviewing!**

* * *

 **Chapter Five**

John stared out over the water, lost in thought.

As far as Doctor Keller was concerned, they'd managed to salvage Elizabeth's mind, everything that made her who she used to be. The rest of his team were in Rodney's lab, taking turns talking to her in the virtual reality. But John couldn't bring himself to believe.

He'd lost her so many times now, first to that stupid Replicator beam, then again to the Replicators after Rodney and Keller had gone behind his back to reactivate the nanites in her blood. When they'd met their Replicator duplicates, he'd learned that his Elizabeth, the real, flesh and blood Dr. Weir, had died, and then he'd watched her Replicator self die as well. And if that wasn't enough, she'd found a way back _again_ , this time as a disembodied consciousness who'd lied to him, led the Replicators back to Atlantis, and then sacrificed herself to right her wrongs.

Death, he was used to. Good people dying was part of his job. But all this back and forth?

It was all too much.

He didn't care what Keller said. The real Elizabeth was dead. All they had left now was what appeared to be a well-crafted copy of her mind, floating around in Rodney's little virtual reality.

Technology. That man honestly believed that technology could solve any problem.

Well, this time, he wanted no part of it. You couldn't bring back the dead. No matter how good the copy...something would always be missing.

* * *

Rodney had stayed longer than Elizabeth would have expected, longer even than Rodney himself had likely expected, but all too soon she found herself once more alone. Sighing, she moved onto the balcony she'd shared with John so many times before, looking out over the vast ocean surrounding the floating city.

She'd known to expect resistance from the city's military leader, but she hadn't allowed herself the luxury of considering just how much his good opinion meant to her. The fact that Rodney had found it necessary to reassure her that he'd come around in time... it spoke volumes for John's current state of mind.

This wasn't just a simple matter of trust. Trust could be earned. But she knew John. If he'd made up his mind that she was more Replicator than human, or, worse still, that she was entirely Replicator, a copy of the original Elizabeth Weir, then this went far beyond the need to earn his trust.

She'd somehow have to prove to him that she _was_ Elizabeth Weir, despite everything that had happened to her in the past two years. And, if she were honest with herself, she wasn't entirely sure that was possible. After everything that'd been done to her... She wasn't so sure herself, anymore, if she was still the same Elizabeth who'd once led the Atlantis expedition.

Maybe she was just an echo of what once was.

* * *

"Sheppard's acting weird," Ronon announced, coming up beside Teyla as she made her way to the commissary for lunch.

"In what way?," Teyla asked, glancing up at her warrior friend.

"He's moping," the Satedan pronounced.

Teyla grinned in spite of herself. "I believe you are right," she agreed.

"Why?," Ronon asked. "We got Weir back. He should be happy."

"He does not believe it is really Dr. Weir," Teyla replied.

"He said that?"

"Indeed."

"Even after Keller confirmed that she is who she says she is?"

"Yes."

"Why?," he asked again. Teyla sighed.

"John's relationship with Elizabeth was...complicated," Teyla explained.

"How? They were friends."

"I believe they may have been more," Teyla said carefully, making sure only Ronon would hear.

The Satedan looked surprised. "Are you sure?"

"No," Teyla said. "But they were close. And it always affected Elizabeth greatly whenever John came close to death on one of our offworld missions."

"That's it?"

Teyla huffed. "It is difficult to explain," she replied. "There was always something there. An attraction between them."

"An attraction?"

"Surely you noticed it as well. They were drawn to each other. At times I thought...but they were always very professional."

"Hmph," he snorted. "So what are we gonna do about it?"

"Do?," Teyla asked, confused.

"About Sheppard. And the mopping."

"I don't think there's anything you or I could do," she replied, grabbing a cafeteria tray and filling it. Ronon did the same.

"Well, we can't just leave him like this," Ronon rumbled beside her.

"Then perhaps you should speak with him, soldier to soldier," Teyla suggested.

"Me? Why me?," Ronon complained.

"Because he will not listen to me," Teyla replied.

"How do you know?," Ronon demanded. "He listens to you all the time."

"Not when it comes to matters of the heart," Teyla replied.

"So you've tried?"

"The last time I spoke to John of this matter, he was weighing opinions. Despite my best effort, I do not believe he has chosen favourably for Elizabeth."

"Talking's not really my thing," Ronon replied.

"Then you will just have to get used to the moping," she said.


	6. Chapter 6

**Chapter Six**

"Mr. Woolsey," Elizabeth greeted, trying to mask her surprise.

"Dr. Weir." He glanced around nervously. "I trust your accommodations are to your liking?"

"A little lonely, at times, but comfortable," she replied candidly.

"Dr. Weir, if I may... I'd like to ask what you intend to do once you've retaken human form."

"I'm not expecting to return to my former position in Atlantis, if that's what you're worried about," she answered, smiling wanly.

"The thought had crossed my mind," Woolsey confessed. "However, that does still leave the question of what you _do_ expect?"

Elizabeth sighed. "Truth be told, I don't know," she replied. "This plan...it was always a long shot. I hadn't really thought much beyond coming to Atlantis for help."

"When you came as a Replicator, would you have joined the others in Ascension?," he asked pointedly. "Or would you have remained on Atlantis?"

"I'm not really ready for Ascension," she confessed. "Though it was preferable to living an eternity without the people I care about, and definitely to spending another moment trapped in subspace."

"Elizabeth..."

"Richard, I don't expect you to go through with this and hand me a job the moment I wake up," she interrupted. "The IOA would never allow it. I've been compromised. I'm a security risk no matter where I go, Earth or Atlantis. I understand that. And if that means having to give up any pretentions to my former career...then so be it."

"So what will you do? What will be the point of all this?," he asked, not unkindly.

"More than anything, I just want the chance to be among friends again. You have no idea what it's like, living among the Replicators. You can see loneliness here, in this virtual reality. But there...imagine being surrounded by all the people of the continental U.S., without a friend among them. That's what it was like, Richard. Even when I joined the group bent on Ascension...there were no real bonds. No loyalty or affection. They had a goal, and they worked toward it. There was nothing more between any of them."

"I'm sorry you had to go through that," Richard replied softly.

"Don't be sorry, Richard. Just give me another chance at being part of something more than a machine," she pleaded.

* * *

"Rodney. What can I do for you?," Dr. Keller asked, putting the last of the bandages on a shelf as the scientist strode into the infirmary.

"I, uh, I was wondering...," he stammered, "If maybe you'd be able to help me with this project?"

"The great Dr. McKay asking for help?," she teased, looking genuinely surprised.

"Yes, well...As it turns out, building a human body is a bit complicated," he replied.

"You don't say?"

"Look, mock if you will, but even with your medical expertise I'm not sure we'll be able to pull this off," he admitted.

"That bad?," she asked.

"I think building a Zero Point Module from the ground up would be simpler, and, frankly, I haven't been able to manage that yet either."

"Is that something you've been working on?," she asked, surprised and a little impressed.

"Of course," he replied, distracted. "My point is, the Ancients were way, way ahead of us in a lot of things. If we really want to save Elizabeth, I'm going to need a _lot_ of help."

"Well, my shift ends in a couple of hours. Why don't we meet for dinner, and we can go over everything we'll need then?"

"Dinner? Really?," he asked, startled.

"It's not a date, Rodney," she replied, realizing how he'd taken her words.

"Oh," he said, deflated. "Of course. Well, dinner...dinner would be good."

She smiled. "You know, if you really wanted a date, all you'd have to do is ask," she said.

"I, uh, I...," he trailed, confused. Jennifer sighed.

"I'll see you in a couple of hours, Rodney," she replied, turning back to her work.

He left without saying another word.

* * *

"You're spending a lot of time out here," Ronon commented, coming up beside John on the balcony.

"Maybe," John shrugged.

"Teyla thinks it's because you're in love."

" _What?!,_ " John demanded, rounding on his friend. The Satedan shrugged.

"Don't ask me. That's just what she said."

"Well, she's _wrong_ ," John snapped.

"So what's on your mind?"

"Nothing," he retorted.

"Doesn't look like nothing."

"Look, I don't pry into your business," John pointed out.

"You do if you think it'll affect a mission."

"And you think I'm going to compromise our next mission?," John bit.

Ronon shrugged. "Maybe. You're pretty distracted."

"I have a lot on my mind."

"Like?," Ronon pressed.

"None of your business."

"It's my business if it's gonna get me killed."

"Look, I really don't want to talk about it," John replied.

"Well, you should," Ronon retorted, walking away.


	7. Chapter 7

**A/N: Sorry about the Wolsey interlude, but it kind of had to be done. :-) In any event, I think tonight's chapter should be more to everyone's liking...**

 **Happy reading, and thank you again for your feedback!**

* * *

 **Chapter Seven**

Elizabeth had no need for sleep, which really only made filling the lonely hours in her virtual Atlantis that much more difficult. Especially since Rodney had programmed very definite day and night cycles, plunging her silent home into darkness every twelve hours. The lights did little to allay the sense that she should be doing something more with her time than sitting here, reading.

She rose, pacing her quarters.

On nights like this, back in the real Atlantis, she would have gone for a walk, inevitably ending up on her favourite balcony overlooking the city. Only there, instead of the quiet stretch of ocean to greet her, John would be waiting.

Somehow, he'd always known when she needed to talk.

She missed those days, those moments, of quiet companionship and simple understanding. It'd taken them a while to find their rhythm, but once they had...John had been one of the best friends she ever could have imagined.

Wrapping her arms around herself, she closed her eyes, just remembering. How many nights had they stood side by side, staring out over the vast expanse of water shimmering beneath the unfamiliar stars, talking about everything and nothing at all until they could relax enough to sleep?

 _Not enough_ , she thought, a pang in her chest. Not enough to quell all the loneliness she felt now.

* * *

John couldn't sleep.

Making his way along the nearly deserted corridors, he pushed out onto the familiar balcony, an old habit he'd never been able to break. Less so since the apparent return of Elizabeth.

He leaned against the railing, taking in the silent night.

Ronon thought he needed to talk. Well, the only person he wanted to talk to was the one who wasn't really here.

He missed her more than he'd ever thought possible. Not that he'd ever thought for a moment that he could truly lose her...

John shook himself. He needed to let go. Needed to accept that she was gone, that he'd failed her.

Needed for everyone to stop saying that that _machine_ was Elizabeth Weir.

Only a part of him, a small part, wanted to believe.

He'd failed her in every way possible. From the reactivation of her nanites to leaving her behind on the Replicator homeworld...he'd failed her. So what right did he have to hope, even just a little, that she'd somehow made it back to them? The truth was, the Elizabeth Weir he'd known and cared for was gone, and had been from the moment the Replicator beam had struck her down. Everything after that...everything after that was a mistake too hideous to bear.

* * *

Elizabeth made it out to the balcony just as the last of the stars gave way to the pre-dawn gloom. She didn't know what she expected, but her skin, or the virtual representation of her skin, tingled with anticipation.

"It's too quiet here."

The voice should have made her jump, but she savoured the rich cadence instead.

"Sometimes," she whispered, closing her eyes.

She could hear him moving closer, feel the warmth of him as he took his place by her side. He didn't say a word, silent so long she feared he really had been just a figment of her imagination.

She opened her eyes to find him watching her quietly.

"Is this a dream?," she asked, reaching out to touch his face. He felt as warm and real as John Sheppard ever had.

"I don't know. You tell me," he replied, not quite shying away, but not quite accepting the touch either. She dropped her hand, holding his gaze instead.

Maybe Rodney had decided she needed something more than a dog for company after all, and come up with this, instead.

"I've missed you," she hazarded, hoping it would reach the real John Sheppard, but not holding her breath.

"Yeah, me too," he said, glancing back out over the ocean. Not much could be seen in the deepening gloom. "Elizabeth..."

"I know. You don't think it's really me." _Anymore than I think it's really you_ , she added silently.

"Truth is, I don't really know what to think," he confessed.

"So don't think at all," she replied evenly.

The look he threw her had so much of the real John Sheppard, it nearly took her breath away.

And then his hands were in her hair and he was kissing her with all the passion and emotion he could muster, and Elizabeth was more sure than ever that this couldn't possibly be the real John Sheppard. Not here, not now, not like this.

"Now I know this is a dream," she said unsteadily, breaking for air.

"You told me not to think," he whispered, leaning his head gently against her own. "This is what happens when I don't think."

Elizabeth chuckled softly, tangling her own fingers through his perpetually unruly hair. "Well, don't start up again on my account," she whispered, capturing his lips once more.

It may not have been real, but it sure beat being alone. She'd have to remember to thank Rodney for the company.

* * *

Rodney walked into his lab, stopping abruptly just inside the door. John lay sprawled across the gurney, haphazardly connected to the virtual reality device, looking for all the world like he'd finally managed to pass out after God-only-knew how many days without rest.

Rodney groaned, pulling readings up from the EEG. "Well, that's not good," he muttered.

"McKay to Keller," he said, tapping his ear piece.

"What is it, Rodney?," the doctor asked.

"Can you come check on Sheppard? It looks like he's unconscious within the virtual reality device."

"I'm on my way."

* * *

The sun was coming up over the balcony, spreading a warm glow across the city, and the two people nestled close together outside.

Elizabeth smiled sleepily, feeling better than she had in a very long time. She felt almost...human.

Beside her, John, or Virtual Reality John, slept curled around her, one arm supporting her head, the other slung protectively around her waist. It felt as comfortable and right as any of the times they'd shared just leaning against the balcony rail together, going over the minutia of the day.

She sighed, absently tracing shapes across his warm, bare chest.

Had this happened two years ago on the real Atlantis, it would have been perfect, she mused. But now...with the feeling that she may only be an echo of the real Elizabeth Weir, and knowing that the real John Sheppard wanted nothing to do with her...there was a hollowness to the illusion, a sad undertone to finally having the one thing she'd never had the opportunity to ask for.

Not that she'd been pining for John Sheppard.

It was more that he'd been her truest friend on the expedition, her partner. An equal, of sorts, in a place where everyone else had looked to her for their next step. It was always hardest when he'd been the one in danger, when it was his life that hung in the balance should negotiations fail.

But she'd never allowed herself to consider him beyond that: a dear friend, and an important asset to the expedition. To do otherwise would have been...unprofessional.

Now, however... She'd been deprived of every aspect of human companionship for two long years. Her allies among the Replicators had been no substitution for actual friendship, or love. And this illusion, this beautiful, peaceful version of John Sheppard, seemed willing to repay it all.

She didn't have it in her to say no, real or not. It just didn't matter anymore, as long as she didn't have to be alone.

* * *

"What the hell?," John shouted, McKay and Keller hovering over him.

"Are you all right?," Rodney asked, ignoring his friend's outburst.

"That depends. Why'd you wake me up?"

Rodney and the doctor exchanged glances.

"You fell asleep in the virtual reality," Dr. Keller explained. "We weren't sure if something had gone wrong..."

"Well, everything was _fine_ ," John snapped.

"We had no way of knowing..."

"Can it, McKay!," John replied, lurching to his feet. "I have work to do."

"Colonel Sheppard," Dr. Keller called, but he was already out the door. "Well, that was odd," she observed.

"Clearly you've never woken him up before," McKay replied with a shrug. "Not so odd, in context."

Jennifer shot him a look. "As far as I can tell, Elizabeth doesn't sleep," she replied, nodding to the virtual reality device. Rodney frowned.

"So when did Sheppard have the opportunity to doze off?," he mused. "Maybe I should visit Elizabeth today, and ask her what happened?"

Jennifer shrugged. "It might be worth a try. Though he may honestly have fallen asleep while visiting, and she just didn't want to wake him. He's been under a lot of strain, after all."

"Yeah. Maybe," Rodney replied, unconvinced.


	8. Chapter 8

**Chapter Eight**

John bolted from the room, doing a quick check to make sure that he did, in fact, have his clothes on.

Of all the times for McKay to give a crap about somebody else...

He shuddered. At least the scientist had walked in _after_ the fact.

Elizabeth.

He stopped dead in his tracks, a cold dread seeping through him.

He'd left without saying goodbye.

You couldn't _do_ what they'd just done and then leave without saying goodbye. It went against every morning-after code of honour he knew.

He turned, looking back toward McKay's lab. How suspicious would it look if he went back there now, long enough to say 'good morning' and 'have a nice day' to Elizabeth before leaving again? McKay was pretty dense when it came to anything involving another human being, but Keller...if Keller was still there, she might catch on.

He didn't want that. The last thing he needed was for everyone else to figure out what he'd done before he'd had the chance to figure it out for himself.

He'd slept with Elizabeth. An Elizabeth?

She'd certainly seemed real enough.

And only Elizabeth could set him at ease like that...

"Sheppard. You lost?"

"What?," he asked, spinning toward the Satedan. Ronon raised an eyebrow.

"Are you all right?," he asked.

"Yeah. Of course. Just...thinking."

"In the middle of the hall?," his friend asked dubiously.

"Yes."

"Whatever. You coming to breakfast?"

"Uh...," Sheppard replied, still thinking of Elizabeth.

"It's a simple question."

John blinked. Coffee would be good. "Um, yeah," he replied, falling into step with the larger man.

"You sure you're all right?," his friend pressed, giving him a funny look.

"Yeah. Fine. Just...tired. That's all."

"You know, if this is still about Dr. Weir, you should just go visit her," the Satedan replied sagely. John's eyes snapped toward him. Was it that obvious?

"You're never going to know if she's real or not if you never bother speaking to her," Ronon finished knowingly.

"Maybe," John said, head reeling. That coffee couldn't come soon enough.

* * *

Rodney entered the virtual reality and looked around. Usually, Elizabeth was close by, wherever he entered. But at the moment, it seemed as if he'd appeared in her quarters, with his friend nowhere in sight.

Rodney frowned. Could the system be malfunctioning?

Elizabeth screamed, clutching a towel tightly about her. "Rodney!," she shouted, glaring at the scientist.

Rodney glued his eyes to the floor, but not before he'd seen enough to start a deep flush up his neck and face. "I...I didn't know," he stammered, keeping his eyes down. "I just came to make sure everything was all right."

"Why wouldn't it be?," Elizabeth asked, grabbing a stack of clothes and retreating into the bathroom.

"I came into my lab this morning to find Sheppard asleep, still connected to your virtual reality," Rodney explained. "I just...I wanted to make sure everything was working all right."

"What?," Elizabeth asked, poking her head back out the door.

"John Sheppard. He was asleep in my lab this morning. Didn't he come to visit last night...?," McKay trailed, feeling increasingly off-balance.

"He wasn't programmed?," Elizabeth asked, a look of slight horror crossing her face.

"Uh, no," Rodney replied, confused. "Like I said before, I didn't even try programming other inhabitants for the city, out of deference to you. I didn't think an illusion could replace the real thing..."

"Oh god," she breathed, looking stricken.

"Why? What happened?," Rodney asked, concerned. "He didn't say anything stupid, did he? Because if he did..."

"Rodney! Can I...can I just have a minute? Please?," Elizabeth asked.

"Uh, yeah. Okay," the scientist replied, stepping awkwardly from the room. "Just, uh...just let me know when you're ready. I'll be out here, waiting."

Elizabeth watched the scientist leave, heart pounding.

It hadn't been a perfectly-timed illusion. It'd been the real thing. The real John Sheppard.

Oh God. She'd slept with John Sheppard. Without preamble. Completely shamelessly.

Oh God. Oh God, oh God, oh God.

This was not good.

And what the hell had _he_ been thinking? Last she'd heard, he'd been having a hard time accepting that she was real.

Hell, _she_ was still trying to get her head wrapped around the concept herself.

Oh, sure, she wanted to believe. Dr. Keller had even given her permission to believe. She had the memories, the personality, the feelings of Elizabeth Weir, after all. All the elements of a matched brainwave pattern.

But with her best friend casting doubt on her, and the gnawing knowledge of just how much the Replicators had manipulated her, manipulated her reality...how could anyone really be sure?

So what exactly had happened last night?

The real John Sheppard had finally made an appearance, and then, what? Decided to throw caution to the wind? Live out some fantasy neither one of them had ever voiced while the chance had been theirs?

She knew what her excuse had been: a sincere need for human contact. But what about him? What could possibly have driven him to kiss her when he had, the _way_ he had, when she'd told him not to think? Despite McKay's incessant teasing to the contrary, as far as she'd ever been able to tell, he'd had little interest in any of the women throwing themselves at him.

So why her? Why now? Why, with so many questions still hanging in the air?

"Elizabeth?," Rodney called, from in the hall. "Is everything all right?"

Shaking herself, Elizabeth dressed in record time, inviting her guest back in.

"I'm fine," she lied at his curious look, only partially engaged in the rest of their conversation that morning.


	9. Chapter 9

**A/N: Heehee, alright, alright...I'll let them talk. ;-) But only 'cause you asked so nicely!**

 **Thank you again to everyone reading and reviewing! Enjoy!**

* * *

 **Chapter Nine**

 **[Spoilers for The Shrine]**

John didn't make it back to McKay's lab until well after dark the next day, between unscheduled missions and freezing cold water...

The upside was, with the scientist in the infirmary with a cold and mild hyperthermia, there was little chance of him being disturbed tonight.

Hooking himself up, he lay down on the gurney, mentally preparing himself for the worst.

"John," she greeted, voice politely neutral. Not a good sign.

"Hi," he said, tucking his hands in his pockets. He swallowed uncomfortably. "McKay woke me up. Before I had the chance to say goodbye," he offered lamely.

"Yes. He came by a little afterward, asking about you."

"Oh."

"John..."

"I swear I wasn't using you," he blurted.

"Then what _were_ you doing?," she asked.

"I...I don't know," he said. "I don't. I just...You told me not to think, and when I wasn't busy trying to figure out if you were real or not, I just...I just wanted to be close."

"We got close, all right," she replied.

"You didn't stop it, either," he pointed out.

She flushed. "I've been at the mercy of machines for two years," she replied carefully. "And when you looked at me the way you did... It's been a long time, John. A really long time since anyone let me get close."

"I'm sorry," he said, shifting awkwardly. "For what you've been through."

Elizabeth glanced away, not trusting her voice. John could see her struggle, keeping quiet until she spoke again.

"I remember being human," she said softly, at last. "I remember how scared I was for you as I lost my hold on Oberoth, and the Replicators regained control. They never told me if you'd escaped or been killed, you know."

"Elizabeth..."

"They killed me the next day," she continued, cutting him off. "The human me. You can imagine my surprise when I woke up in another body, mine, but not. They had more control over my Replicator self. Could monitor and curtail my movements more easily. My own body became a jail cell."

John stood frozen, listening.

"I've been through a few incarnations now," she continued, shaking her head. "And I've been copied and...changed...a few times besides."

"But you're not a copy," he said, understanding at last. She shrugged.

"I remember being human," she repeated. "But that doesn't mean...," she cut off.

It pained him to think that she doubted herself. There was no denying the Elizabeth-ness of the woman standing before him. Even if everyone closest to her was still waiting to see if this was too good to be true...Himself included.

"Come here," he whispered, pulling her into his arms.

Elizabeth let him hold her, surprised by how reassuring it felt just to have him trust her enough to let her get this close again.

Maybe the other night hadn't been just a fluke...

"So what now?," she asked gently, still holding on. Reveling in the warm solidity that was John Sheppard.

"Now we let Rodney do what Rodney does best," John replied. "He'll get you out of here, and then..."

"And then.," Elizabeth repeated meaningfully. He knew as well as she did that nothing could be the same after this. Atlantis had long since changed hands, and didn't need her anymore. And the IOA...the IOA would likely never trust her, no matter how many of her former people were willing to vouch for her identity.

"And then you'll do what you do best," John answered into her hair, his words tickling her left ear. "You'll convince them of who you are. You'll go back to being the brilliant diplomat, and the negotiations mastermind."

Elizabeth smiled sadly. "Have I managed to convince you, John?," she asked, already knowing the answer.

"I want to believe," he sighed, and she could feel the depth of his words in the way his chest rose and fell beneath her cheek.

"But you still have your doubts," she answered sadly.

"Usually if something is too good to be true, it isn't the real thing."

She pulled away, meeting his gaze. "And this is too good to be true?," she asked softly.

"You, alive? Yes," he said, holding her gaze. "And this?," he added, indicating their current proximity, "Hell, yes."

"You never said anything," she said, smiling in spite of herself.

"You were my boss," he answered with a small shrug. "And contrary to popular belief, I'm not actually very good at the whole relationship thing."

Elizabeth raised an eyebrow. "No?," she asked gently.

He shook his head. "My first marriage was a mess," he answered truthfully. "I had no idea how to be a husband. And honestly, it wasn't long before I stopped even trying. It was easier to take extra missions than it was to be home." He shrugged again. "I've never really blamed Nancy for leaving. It was sort of a relief."

"Well, if it makes you feel any better, I left my partner with a Dear John recording, telling him I'd taken a job in another galaxy without so much as a by-the-by sort of warning beforehand."

"Ouch," he said.

"Yeah. So, maybe you're not the only one here who's not very good at the whole relationship thing."

John smiled, leaning his forehead against her own.

"So what now?," he asked, echoing her earlier words.

"We have an entire virtual reality all to ourselves," she replied, mirroring his smile. "I say we explore the possibilities."

"I like the sound of that," he murmured, kissing the bridge of her nose.

Elizabeth chuckled softly, capturing his lips with her own. "Me too," she whispered, a thrill of excitement shooting up her spine as he responded in kind. _Me too_.


	10. Chapter 10

**A/N: Three more chapters after this, and an epilogue. :-) Thank you as always for your very kind reviews!**

* * *

 **Chapter Ten**

"Sheppard's acting weird," Ronon declared.

"So you have said before," Teyla remarked, carefully balancing Torren in one arm as she attempted to eat her breakfast.

"This is different," he answered. Teyla sighed.

"It seems to me that the Colonel is more at peace with himself these days," she replied. "Perhaps you should be, as well."

"He's sleeping in McKay's lab," Ronon said bluntly. Teyla frowned.

"He is?"

"Yeah. Every night since just before McKay got sick."

Teyla's brows knit together. "Are you certain?," she asked.

"I see him coming out of there every morning," Ronon replied. "And he's never had his coffee yet."

"Perhaps he is simply visiting Elizabeth before his shift begins?," Teyla suggested.

"Or maybe there's something else going on," he said.

"Ronon. Whatever Colonel Sheppard is doing in Rodney's lab is none of our concern. It is still preferable to him brooding out on the balcony each day."

"It's weird."

"There was a time when he and Elizabeth were very close," Teyla reminded him. "Perhaps with everything that has happened with Rodney, John needed the comfort of a true friend."

"We're his friends," Ronon noted gruffly. "And since when does he even believe that's the real Elizabeth?"

"Perhaps since he took the time to speak with her," Teyla replied evenly. "There is much of the Elizabeth Weir I remember within Rodney's virtual reality."

"I know," Ronon replied. "But still."

"If you wish to know what is really going on, perhaps you should speak with the Colonel," Teyla advised. "I see no harm in John spending time with an old friend, especially given everything we have been through these past few weeks."

"Maybe I will," Ronon retorted, stabbing a piece of food from his plate.

* * *

Elizabeth smiled warmly at her morning guest. She hadn't seen the doctor in weeks, ever since Rodney had been diagnosed with the Second Childhood. She had missed the young woman's easy manner and friendly chats.

"I hear that you managed to save our Rodney," Elizabeth said, still grinning at the news John had brought her just the night before.

"It was Ronon, actually," Dr. Keller confessed sheepishly. "I really didn't believe him about the Ancient shrine. If it hadn't been for his insistence, and Jeanie's belief, McKay would still be..." She stopped, at a loss for words.

"Well, I'm just glad everything worked out," Elizabeth answered reassuringly.

"Yeah, me too," Jennifer sighed.

"Is something wrong?," Elizabeth asked, noting the slight look of defeat in the doctor's stance.

"It's just...When he was sick. McKay said some things...Some things I wish could be true."

"Such as?," she pressed.

"He told me he loves me," Keller said in a rush. "But he was already starting to forget a lot by then. And he'd never really even hinted at anything before..."

Elizabeth smiled brightly. "Not to the person who needed to hear it, maybe," she replied, remembering some of her own chats with the scientist. "But Rodney can never keep his thoughts to himself for long."

Jennifer blinked in surprise. "Did he say something to you?," she asked, hope filling her voice.

Elizabeth only smiled. "Just give him some time," she said, giving the doctor's hand a gentle squeeze. "He'll find the courage to tell you again."

"I hope so," the doctor confessed. Then, "I'm really sorry I haven't been visiting. I've just been so worried, trying to find a solution..."

"I know," Elizabeth replied understanding. "And it's all right. Really. I haven't been alone."

The doctor looked surprised. "Really? I thought Rodney and I were your main visitors," she said, flushing slightly at how that sounded.

Elizabeth laughed. "You were. Then John started dropping by."

"Colonel Sheppard?," the doctor squeaked. "He hasn't been giving you a hard time, has he? Because I could have Ronon talk to him..."

Elizabeth shook her head. "He's been...wonderful," she confessed, smiling.

Jennifer's jaw dropped. "Are you...? I mean, not that it's any of my business, but are the two of you...together?," she asked awkwardly.

Elizabeth grinned. "We're...something," she replied happily. "We'll just have to see how things go, I guess."

* * *

Ronon was waiting outside McKay's lab when John reached the door.

"Ronon," he greeted, frowning slightly at the large Satedan's defensive stance.

"What are you doing in here every night?," Ronon demanded, skipping right to the point.

"Visiting Elizabeth," John replied honestly.

"Every night? All night?," Ronon asked skeptically.

John shrugged, acutely conscious of the fact that Ronon was coming uncomfortably close to the truth.

"So when do you sleep?," the Satedan asked.

"At night. Like everyone else," John replied easily.

"In the virtual reality?"

"Look, what difference does it make?," John demanded. "First everyone kept telling me to just come talk to Elizabeth, and now you're questioning the amount of time I'm spending with her?"

"Is it her?," Ronon asked.

John froze. She was so much the Elizabeth he remembered, warm, intelligent, funny. And so much more, besides. In just a few short weeks, she'd reintegrated herself as an integral part of his life, the voice of reason in a galaxy that made so little sense sometimes.

"Yes," he answered at last, not knowing what else to say. How could he deny it now? She was, in every way that mattered, Elizabeth Weir. And he was quickly realizing just how much she'd always meant to him. How much he'd really lost when he'd lost her...

Ronon looked surprised. "Are you two a couple then?," he asked, blunt as ever.

John felt himself colour slightly. "What difference does it make?," he asked, rather than answer the question. Ronon shrugged.

"Just curious."

"Well, it's really none of your business," John retorted.

Ronon frowned. "If you keep this up, other people will notice. And they'll start to talk," he warned.

"I know," John sighed.

Ronon eyed him carefully. No doubt looking for signs that he'd somehow been compromised.

"Just be careful," the Satedan grunted at last, pushing away from the door.


	11. Chapter 11

**Chapter Eleven**

 **[Spoilers for The Shrine]**

Three weeks. He'd lost three weeks of work on solving Elizabeth's housing situation while slowly losing his mind to the Second Childhood.

Zalenka had made absolutely no progress either, while he'd been out of the game.

And Keller...well, she'd been a little busy trying to save him, he conceded.

Still. The specs on this project were enormously complicated. And he'd just added three weeks to her wait. If not more. Parts of his memory were still a little hazy...

Elizabeth deserved better. He owed it to her.

She wouldn't be in this mess if it hadn't been for him.

"Need any help?," a voice asked from just inside the door.

He glanced up sharply, a snide remark on his tongue when he noticed who was there.

"Jennifer," he replied, surprised. She smiled.

"I have another couple hours before my next shift starts," she explained.

"Pull up a seat," he replied, indicating the space beside him. "I was just trying to remember where I left off," he added nervously.

The doctor shot him a sympathetic smile. "You should be able to remember everything with your usual clarity within the next few days," she reassured.

"Let's hope so," he replied, glancing back at the specs. "Otherwise, someone will have to explain to Elizabeth that I've failed her again."

"It's not Elizabeth I'd worry about," Jennifer replied, earning a confused frown from the scientist. "She's the forgiving sort," Jennifer answered easily. "But the Colonel? I wouldn't want to be the one telling him."

Rodney blinked slowly, trying to piece together what she'd just said.

"Wait a minute," he said. "Are you saying...Are you saying that Sheppard and Elizabeth are _involved_?," he asked.

"It certainly sounds that way," Jennifer confided. "I spoke with Elizabeth just yesterday, and she said the Colonel's been by every day since just before you got sick."

Three weeks. God, just how much had he missed?

"Huh," he replied, taken aback. "I mean, I always thought there was something between them, but...Huh."

"I think it's wonderful," Jennifer replied, grinning. "You should see how much happier she looks, just talking about him."

"Really?"

"Mmm-hmm."

Sheppard hadn't seemed any different to him, but then again...he hadn't exactly been himself the past three weeks.

"I'm glad she's happy," he said instead, repositioning the schematics to sit between them. Jennifer sighed.

"Yeah. It must be nice to have someone," she replied, giving him a meaningful look.

Rodney froze. "I...um...I imagine it is," he stammered at last, looking away.

Jennifer sighed again, bringing her focus down to the schematics spread out before them.

Was it his imagination, or did the doctor looked...disappointed?

* * *

Weeks quickly wore into months, and the machine needed to give Elizabeth her life back was still only in the preliminary stages of construction, at best.

Rodney dug his palms into his tired eyes, trying to get them to focus properly on the project.

"Maybe we should call it a night," Jennifer suggested, noticing the gesture.

"I wish we had something left of her. Something we could use to just clone her," Rodney grumbled, frustrated. "I mean, we have the entire Asgard database at our disposal, and all the knowledge of the Ancients, and I'm still struggling to wrap my head around some of the basics here."

"Creating a fully developed adult clone wouldn't be much simpler," Jennifer pointed out gently.

"Michael did it," Rodney snarked.

"Yeah, and Becket still needs weekly injections to keep his cells from degrading," Jennifer reminded him. "Besides, we don't have any genetic material left," she added, shaking her head. "I have countless images, scans, x-rays, you name it. But nothing we could use to create a clone."

"This is going to take us _years_ ," Rodney complained, indicating the partially built machine.

"I think Elizabeth understands that," Jennifer soothed.

Rodney snorted. "You know what the worst part of that statement is?," he asked. "Elizabeth knows these specs inside and out. If Woolsey would approve it, she could have this thing built in a fraction of the time, using a Replicator body."

"I don't think Elizabeth would approve of that any more than Mr. Woolsey," Jennifer countered. "She was the one who said the Replicators couldn't be trusted, even with all your safeguards in place."

"Yes, but the other Replicators are gone. She'd be the only one, and we could destroy the body as soon as she had one of flesh and blood."

Jennifer shook her head. "I know how you feel, Rodney," she said, "But I don't think they'd go for it."

"We've been working on this for three months now. _Three months_. And I don't feel like we're any closer to having a working device than we were when we started."

"Are there any other scientists you could bring into the project?," Keller asked.

Rodney shook his head. "Zalenka is already helping in his spare time, and the only other people who might have enough mathematical background to sift through this are Colonel Carter and my sister. And right now, Carter's pretty busy with the Ori problem back on Earth."

"What about your sister?"

"I can't ask her to do this," Rodney said. "I can't ask her to leave her family for that long. It would kill her."

"What if she could bring them here? To Atlantis?," Jennifer asked.

Rodney blinked, surprised. "No one else was allowed to bring family," he pointed out.

"Everyone else thought this would be a one-way trip to another galaxy," Jennifer reminded. "Things have changed. There are transports between Pegasus and the Milky Way every month. Plus there's always the Stargate."

"It's too dangerous," Rodney said. "I mean, between the Wraith, rogue Asgards, and the likes of Michael, I could never ask her to bring her family here. This place is a death trap."

"Then maybe we should bring our work to _her_ ," Jennifer suggested.

"You mean leave Atlantis?"

"For a while," Jennifer said with a shrug. "Just long enough to get some help with this project."

"We're both department heads. We can't exactly just up and leave," Rodney pointed out.

"Maybe not, but would it really hurt to ask? I'm sure Dr. Becket could be persuaded to come back long enough to keep the infirmary from being overrun, and Zalenka could always take over for you."

"Mmph," Rodney grunted, not entirely liking the idea of being replaced by Zalenka.

"Just think about it, all right?," Jennifer pleaded. "We need the help, you said so yourself."

"All right," Rodney sighed. "I'll think about it."

"Good," Jennifer said, looking a little happier. "Now, go get some rest. You look like hell, and I'm not far behind."


	12. Chapter 12

**A/N: Just about to the end, now. Tomorrow I'll post the final chapter and epilogue to tie things up. As always, thank you to everyone for reading and reviewing! Your feedback and encouragement has been amazing!**

* * *

 **Chapter Twelve**

 **[Minor spoilers for Brain Storm – some lines reused, no copyright infringement intended]**

John felt a thousand different emotions as he launched himself into the virtual reality, but near the top of his list was an almost overwhelming urge to hit Rodney.

"John, are you all right?," Elizabeth asked, immediately picking up on his agitation.

"It's McKay," John growled, pacing the length of the room. "He wants to take the project back to Earth. Take _you_ back to Earth," he stressed.

"And this is a problem?," Elizabeth replied softly, watching him pace.

"I feel like I just finally got you back, and he's going to take you away again," John said, scrubbing his hands across his face, through his messy hair.

"Hey, it's all right," Elizabeth soothed, reaching out to touch his arm. "Rodney already told me the plan. He thinks it'll speed up the work on the device if he can consult with Jeannie and Sam."

John snorted. "Did he also mention that it could still take _months_? We've already lost two years thanks to his brilliant plan on the Replicator homeworld. How much more does he plan to take?"

" _John_ ," Elizabeth warned. "If it hadn't been for those two years apart, nothing ever would have changed. I'd still be your boss. And none of this would ever have happened," she said, indicating the space between them. "Is that what you'd really want?"

"I can't lose you, Elizabeth. Not again."

"You _won't_ ," she said, smiling in spite of herself. "Not for long, anyway. And the next time we meet, it won't be in a virtual reality. I'll be _myself_ again."

"So you're okay with this?," he asked, not fully convinced.

She stepped closer, gently cupping his cheek in her hand. "I'm okay with the idea of someday being able to hold you for real," she said softly. "Of being together as often as we want."

He had to concede that point. As much as they'd loved spending every night together in the virtual reality, Ronon had been right. It'd been too obvious, even if they had taken things slow after that first night. And right now, seeing each other meant stolen evenings between Rodney's never-ending research in the lab, and his team's constant off-world trips.

"John."

"I know," he sighed, letting his arms relax enough to pull her closer. "But I still don't have to like it."

Elizabeth smiled. "Just keep yourself safe," she whispered. "Rodney will figure this out, and then we'll have all the time in the world."

* * *

John watched quietly from the control room as Drs. Keller and McKay carefully arranged Elizabeth's virtual reality by the 'gate.

They'd said their goodbyes the night before, the doctors reluctantly giving them the privacy they needed before everything got packed up for transport. There'd been very little left to say when the time had come, but they'd enjoyed every moment together just the same.

McKay was hopeful it wouldn't be long now, but John wasn't so sure.

The 'gate came to life below, the soft blue glow casting bathing the equipment and casting long shadows across the floor. Rodney turned to look up at him, giving a reassuring nod before grabbing his share of the gear and stepping through.

" _I know what she means to you_ ," he'd said when John had disconnected the night before. " _I'll have her out as soon as I can."_

"She will be all right, John," Teyla said softly from his side. "Rodney will not fail her again."

 _Be safe_ , he prayed silently, heart in his throat as she passed through the event horizon.

* * *

Life on Earth was a lot lonelier than it had been on Atlantis, even if her own surroundings hadn't really changed. There were fewer people here who knew her well enough to visit, and the ones who did were almost always busy trying to save her.

She had the best and brightest people of two galaxies working on her problem, but she missed John, missed Teyla and Ronon and all the others who used to stop by. Books and movies were a very poor substitute for the companionship she craved.

She'd lost track of how long she'd been there, in her virtual Atlantis. Some days, as much as she appreciated everyone's efforts, Elizabeth wished she could just disconnect. Turn herself off. Avoid the endless, empty hours alone.

"Dr. Weir."

Elizabeth whirled around, startled by the sudden, unexpected intrusion.

"General O'Neill?," she asked, surprised by his appearance.

"Sorry it took me so long to drop by," he offered apologetically. "I've been meaning to for a while now."

"Washington keeping you busy?," she teased.

"Oy. Don't even get me started on that bag of rats," he grumbled. "How are _you_ doing?"

"Oh, you know. Keeping busy," she lied.

"You're bored silly," he guessed.

"Is it that obvious?"

The General shrugged. "Hey. You're talking to the king of boredom, here."

She quirked an eyebrow, and he frowned. "You know what I mean," he said.

"So what brings you to my neck of the woods, General?"

"John Sheppard."

"John?"

"He's tenacious, I'll give him that," the General said.

Elizabeth looked at her guest nervously. "What exactly has he been asking for?," she asked, keeping her voice as level as possible.

"Oh, any number of things," The General replied vaguely. "You know. Back pay for the past two years, reinstatement on Atlantis. Nothing I wouldn't have asked for had you been a member of my own team," he reassured.

"I never asked him to speak on my behalf," Elizabeth began.

Jack snorted. "I know. You would have been _subtle_."

"I'm really sorry..."

"Don't be. I happen to think he's right. Mostly."

"Mostly?"

"Don't get me wrong. You were always the best choice for Atlantis. But circumstances have changed."

"What are you getting at, General?"

"Woolsey is doing a remarkably good job of keeping the IOA in line, which I appreciate. I also understand there might be a personal agenda behind the Colonel's championship of your case?"

"Yes, Sir," she confessed, wincing slightly.

"Congratulations," Jack offered, a slight grin tugging at his mouth. "My point is, I can't give Atlantis back to you. Not as expedition leader."

"I understand that, General."

"However," Jack continued, "I _have_ been authorized by the President to offer you a position on Atlantis as lead Diplomat. You'll answer directly to Wolsey, and work with whichever teams require your expertise."

"That's a very generous offer."

"Yes, it is," the General agreed.

"What's the catch?"

Jack smiled. "Once the IOA gets wind of this, they'll almost certainly insist on an evaluation period, and you can bet they'll work damn hard to discredit you every chance they get. You and I both know how powerful a motivating factor fear can be."

"Mmm," she agreed.

"Take the job, Elizabeth."

"And if I pursue things with John?"

"You both answer to Wolsey, not each other. I don't see a problem," he shrugged.

"It sounds too good to be true."

"Yes. Well. The eggheads still need to find a way to get you out of _here_ , first," he reassured.

Elizabeth grimaced. "In that case, I accept."

"Good," Jack smiled. "Sheppard will be _delighted_."

"What exactly did he _say_ to you?," she laughed.

"Ah. A General never kisses and tells," he winked.

* * *

"Ah, Jennifer," McKay greeted, coming in to their shared lab at the SGC. "I was hoping I'd find you here."

"Is everything okay?," she asked, looking him up and down. "You look a little shaky."

"What? Oh. That's nothing," he said. "It's just, I was wondering...I mean, there's this conference thing that I've been invited to and, well...Everyone will be there. I mean, everyone who's anyone in the physics community will be there..."

"Rodney," she interrupted.

"Yes?"

"Breathe."

"Right. Well, anyway, the other physicists think I'm a bit of a joke, because, well, I do _this_ for a living and nobody knows. So I was thinking that if I went, and maybe brought someone...a beautiful someone," he amended nervously, and Jennifer smiled, "that maybe they'd all take me a little more seriously," he finished.

"Are you asking me on a _date_?," Jennifer teased.

"Well, ah, maybe. Yes. I'm asking you on a date." He looked like he might faint.

"I'd love to go," she smiled, and the physicist breathed a deep sigh of relief.

"That's...that's great," he said. "It's this Friday. Black tie, if that's okay."

"I look forward to it," she laughed.


	13. Chapter 13

**A/N: Well, this is it, the final day of posting. This was my first attempt at SGA fanfic, but I've really loved writing this story, and by the sounds of it, others have loved reading it too. :-) Thank you all again for all your very kind reviews, and I hope you like the ending!**

* * *

 **Chapter Thirteen**

 **[Spoilers for Enemy At The Gate]**

The whole freaking universe was out to get him.

As if the Wraith weren't bad enough all on their own, they now faced a hive powered by an Ancient ZPM. A hive, he might add, that now also had the coordinates to Earth, thanks to some seriously screwed up multi-verse radio traffic.

"Pack your bags," Woolsey advised. "You've just been re-assigned to the weapons' platform at Area 51."

"Earth? You're sending me to Earth?," John asked, startled.

"Within the half hour," Woolsey replied.

 _Elizabeth._

"Colonel Sheppard," General Landry greeted from the other side. "Nice of you to drop by."

"Not a problem, Sir."

"Your transport is ready and waiting."

"Already?," he asked, crestfallen.

"Already," the General confirmed.

And then, of course, without so much as a moment to regain his equilibrium, things went from bad to worse

* * *

"Dr. McKay. You're needed in the Control Room."

"What? Why?," the scientist asked, distracted.

"General Landry says we need a plan B."

"Plan B? What was plan A?," Rodney snapped.

"The Ancient weapons platform at Area 51."

"Weapons platform? Are we under attack?," the scientist asked, his voice rising an octave with sudden worry.

"From the Wraith," the Airman confirmed. "The weapons' platform was destroyed."

" _What_? _How_? Why wasn't I informed of this sooner?"

"I don't know, Sir," the Airman sighed. "Please come with me."

* * *

"We've lost contact with Sheppard," Control announced. "He's on an intercept course for the hive."

"He can't take on a hive!," Rodney screeched. "What the hell is he thinking?"

"Colonel Sheppard," Control hailed. "If you can hear us, break off pursuit. I repeat, break off pursuit."

No answer.

Rodney's heart hammered in his chest. This couldn't be happening. Not when they were _so_ close. Sheppard couldn't die now. Not like this.

"John!," he yelled, grabbing the microphone from the nearest tech. "You _have_ to turn back!"

"I'm a little busy, Rodney," the pilot ground out in reply.

"Getting yourself _killed_ is not 'a little busy'!"

"Blowing up this damn hive _is_ ," John answered firmly. "Who gave you a mic, anyway?"

"Does it _matter_?," Rodney demanded.

"Get off the comm, Mckay," the pilot ordered. "Before you get yourself in trouble."

"What about you?"

Silence.

"John?"

"Tell Elizabeth I'm sorry," he said. Then the channel went dead.

* * *

Elizabeth stood out on the balcony, overlooking the endless ocean below. She'd been restless all day, a bundle of nervous energy with nothing to do, and nowhere to be.

It was an old feeling, this, as familiar and well-worn as her expedition uniform had once been. Something was wrong.

 _John. What have you done now?_

* * *

John armed the warhead, switching on a comm channel.

"This is Colonel John Sheppard, to any friendlies," he said. "You might want to stand back for this."

"John?," came Teyla's startled voice.

"Get out of here, Teyla. That's an order," John replied, surprised Atlantis had made it close enough to hear him.

"Colonel. We are on the ship. Where are you?"

"On the ship," he replied, confused. "How'd you get here?"

"That is a long story, and we have little time."

"Right. Well, can you get off?"

"Yes," she replied patiently. "As can you. We must rendez-vous."

"And if this is some sort of Wraith trick?"

"Then it will be a short meeting indeed," he heard the Athosian smile wryly. "Give yourself enough time before detonation. Hone in on my signal. We will be waiting at our point of departure."

* * *

"I can't watch," Rodney said, turning away. The countdown ticked resolutely into oblivion, set according to John's last transmission.

No one in the control room breathed.

"SGC, this is Atlantis. We have them!," Woolsey's voice crackled triumphantly over the open comm channel. Moments later Control shouted, "We have a hit! The hive is coming apart!"

Rodney slumped against the wall, the tension of the last few minutes draining from his over-tired body. Everyone around him burst into cheering applause.

"Control, this is Atlantis base. Requesting permission to land," Woolsey asked over the celebratory din.

"Permission granted, Atlantis. Tell Sheppard to bring her in nice and easy."

* * *

"Hey," he said, startling her where she stood on their balcony.

"John! What are you doing here?," she exclaimed, lighting up.

"It's a long story," he said, offhand, "but I was in the neighbourhood and I wanted to stop in and say 'hi'."

She closed the distance between them, wrapping him in a tight embrace. "Hi," she breathed into his ear.

He put his own arms around her, holding her close. "Hi."

They held on to each other for a while before Elizabeth pulled ever so slightly away. "I almost lost you today, didn't I?," she guessed, searching his eyes for the truth.

"It was looking pretty bad for a while," he confessed.

She traced the outline of his face, relishing the feel of him. "You're never going to stop taking chances, are you?," she asked, meeting those puppy dog eyes..

"It's part of who I am," he answered, almost apologetically.

She sighed, never releasing her hold. "Just promise you'll keep coming back," she murmured, leaning closer so that her warm breath tickled his neck. John smiled.

"For you? Always."


	14. Epilogue

**Epilogue**

Elizabeth opened her eyes, not fully recognizing her surroundings.

"Hey," John smiled, stepping into view. "How are you feeling?"

"A little disoriented," she admitted shakily. "Where am I?"

"The infirmary, at the SGC."

"I'm alive?," she gasped, touching her own face.

"And as beautiful as ever," he replied earnestly.

"Nobody said..."

"I know. Rodney thought the transfer would go better if you were completely at ease."

"And did it?," she asked, sitting up.

"You tell me."

"I feel like me."

"That's a good sign."

"John?"

"Yes?"

"What are you wearing?"

John looked down, taking in his tuxedo. "Wedding clothes," he grinned.

"It's a little soon, don't you think?," she retorted.

The Colonel chuckled. "For us, maybe. But there's a dress for you, too, if you want to come."

"Are you asking me on a date?," she smiled.

"I guess I am."

Elizabeth beamed. "Then the answer is 'yes.' I'd love to go."

"Don't you want to know who's getting married?," he teased.

"I suppose it would be polite," she agreed, climbing off the bed to stand toe to toe with the Colonel.

John grinned, gently caressing her cheek with his hand. "I guess _you_ could call them 'mom' and 'dad'," he answered lightly, his eyes so full of admiration she nearly lost the words.

"My _what_?," she asked a moment later, and John laughed.

"Come on," he chuckled, guiding her past smiling infirmary staff. "Mckay'll kill me if we're late. I've got the rings!"

* * *

Three years after her death, Elizabeth had never felt so _alive_. Surrounded by all the friends she knew and loved best, and with John Sheppard firmly by her side, she was positive it'd all been worth it to come to this point.

"I love you," John murmured softly, taking her hand, and Elizabeth smiled.

"I love you, too," she said, eyes swimming happily as she laid her head on his shoulder, watching with all the others as Rodney and Jennifer shared their first dance as husband and wife.


End file.
